Publications

Google Scholar

2016

1. Silva GGZ., Alvares, F. & Edwards, R. A. An agile functional analysis of metagenomic data using SUPER-FOCUS. Springer Book chapter - Methods in Mol. Biol. (2016) (accepted)

2. Silva GGZ, John Matthew Haggerty, Daniel A. Cuevas, Michael Doane, Elizabeth A Dinsdale, Bas E. Dutilh, and Robert A. Edwards: Ecological Implications of Metagenomics Data Analysis (under-review)

3. Adriana Sturion Lorenzi, Genivaldo G. Z. Silva, Fabyano Alvares Cardoso Lopes, Mathias Ahii Chia, Robert A. Edwards, and Maria do Carmo Bittencourt-Oliveira: Draft genome sequence of the saxitoxin-producing cyanobacteria Cylindrospermopsis raciborskii ITEP A1 from a Brazilian semi-arid freshwater body revealing cylindrospermopsin synthetase Genes. Genome Announc. 2016 May-Jun; 4(3): e00228-16.

2015

1. Silva GGZ, Green K., B. E. Dutilh, and R. A. Edwards: SUPER-FOCUS: A tool for agile functional analysis of shotgun metagenomic data. ( 2015 Oct 9. pii: btv584.)

2. T. David Matthews, Robert Schmieder, Genivaldo G. Z. Silva, Julia Busch, Noriko Cassman, Matthew Doherty, Dawn Green, Brian Matlock, Brian Heffernan, Gary Olsen, Leigh Farris Hanna, Dieter Schifferli, Stanley Maloy, Elizabeth A. Dinsdale, and Robert A. Edwards: Genomic Comparison of the Closely-related Salmonella enterica Serovars Enteritidis, Dublin and Gallinarum ( 2015 Jun 3;10(6):e0126883. doi: 10.1371/journal.pone.0126883).

3. Edmundo Calva, Claudia Silva, Mussaret Zaidi, Alejandro Sanchéz-Flores, Karel Estrada, Genivaldo Gueiros Z. Silva, Mayela Soto-Jiménez, Magdalena Wiesner, Marcos Fernández-Mora, Rob Edwards, and Pablo Vinuesa. Complete genome sequencing of a multidrug-resistant and human-invasive Salmonella enterica serovar Typhimurium strain of the emerging ST213 genotype  ( 2015 Jun 18;3(3). pii: e00663-15. doi: 10.1128/genomeA.00663-15).

4. Acacio A. Navarrete, Tatiana R. Diniz, Lucas P. P. Braga, Genivaldo Gueiros Z. Silva, Julio C. Franchinic, Raffaella Rossettod, Robert A. Edwards, Siu M. Tsai. Multi-analytical approach reveals potential microbial indicators in soil for sugarcane model systems ( 2015 Jun 9;10(6):e0129765. doi: 10.1371/journal.pone.0129765).

2014

1. Silva GGZ, Cuevas DA, Dutilh BE, Edwards RA: FOCUS: an alignment-free model to identify organisms in metagenomes using non-negative least squares. ( 2014 Jun 5;2:e425. doi: 10.7717/peerj.425).
2. Silva GGZ, Dutilh BE, Edwards RA: FORMAL: A model to identify organisms present in metagenomes using Monte Carlo Simulation. bioRxiv 2014:010801.
3. Lim YW, Cuevas DA, Silva GGZ, Aguinaldo K, Dinsdale EA, Haas AF, Hatay M, Sanchez SE, Wegley-Kelly L, Dutilh BE, Harkins TT, Lee CC, Tom W, Sandin SA, Smith JE, Zgliczynski B, Vermeij MJA, Rohwer F, Edwards RA: Sequencing at sea: challenges and experiences in Ion Torrent PGM sequencing during the 2013 Southern Line Islands Research Expedition. ( 2014 Aug 19;2:e520. doi: 10.7717/peerj.520).
4. Dutilh BE, Thompson CC, Vicente AC, Marin MA, Lee C, Silva GGZ, Schmieder R, Andrade BG, Chimetto L, Cuevas D, Garza DR, Okeke IN, Aboderin AO, Spangler J, Ross T, Dinsdale EA, Thompson FL, Harkins TT, Edwards RA: Comparative genomics of 274 Vibrio cholerae genomes reveals mobile functions structuring three niche dimensions. ( 2014 Aug 5;15:654. doi: 10.1186/1471-2164-15-654)
5. Dutilh BE, Cassman N, McNair K, Sanchez SE, Silva GGZ, Boling L, Barr JJ, Speth DR, Seguritan V, Aziz RK, Felts B, Dinsdale EA, Mokili JL, Edwards RA: A highly abundant bacteriophage discovered in the unknown sequences of human faecal metagenomes. ( 2014 Jul 24;5:4498. doi: 10.1038/ncomms5498)
6. Junior NA, Meirelles PM, Santos E de O, Dutilh B, Silva GGZ, Paranhos R, Cabral AS, Rezende C, Iida T, Moura RL de, Kruger RH, Pereira RC, Valle R, Sawabe T, Thompson C, Thompson F: Microbial community diversity and physical–chemical features of the Southwestern Atlantic Ocean. ( 2015 Mar;197(2):165-79. doi: 10.1007/s00203-014-1035-6)

2013

1. Silva GGZ, Dutilh BE, Matthews TD, Elkins K, Schmieder R, Dinsdale EA, Edwards RA: Combining de novo and reference-guided assembly with scaffold_builder. ( 2013 Nov 22;8(1):23. doi: 10.1186/1751-0473-8-23)
2. Thompson CC, Silva GGZ, Vieira NM, Edwards R, Vicente ACP, Thompson FL: Genomic Taxonomy of the Genus Prochlorococcus. ( 2013 Nov;66(4):752-62. doi: 10.1007/s00248-013-0270-8).
3. Garcia GD, Gregoracci GB, Santos E de O, Meirelles PM, Silva GGZ, Edwards R, Sawabe T, Gotoh K, Nakamura S, Iida T, Moura RL de, Thompson FL: Metagenomic Analysis of Healthy and White Plague-Affected Mussismilia braziliensis Corals. ( 2013 May;65(4):1076-86. doi: 10.1007/s00248-012-0161-4).
4. Trindade-Silva AE, Rua CPJ, Andrade BGN, Vicente ACP, Silva GGZ, Berlinck RGS, Thompson FL: Polyketide Synthase Gene Diversity within the Microbiome of the Sponge Arenosclera brasiliensis, Endemic to the Southern Atlantic Ocean.( 2013 Mar;79(5):1598-605. doi: 10.1128/AEM.03354-12).

2012

1. Cassman N, Prieto-Davó A, Walsh K, Silva GGZ, Angly F, Akhter S, Barott K, Busch J, McDole T, Haggerty JM, Willner D, Alarcón G, Ulloa O, DeLong EF, Dutilh BE, Rohwer F, Dinsdale EA: Oxygen minimum zones harbour novel viral communities with low diversity. ( 2012 Nov;14(11):3043-65. doi: 10.1111/j.1462-2920.2012.02891.x).
2. Oliveira LS de, Gregoracci GB, Silva GGZ, Salgado LT, Filho GA, Alves-Ferreira M, Pereira RC, Thompson FL: Transcriptomic analysis of the red seaweed Laurencia dendroidea (Florideophyceae, Rhodophyta) and its microbiome. ( 2012 Sep 17;13:487. doi: 10.1186/1471-2164-13-487).
3. Trindade-Silva AE, Rua C, Silva GGZ, Dutilh BE, Moreira APB, Edwards RA, Hajdu E, Lobo-Hajdu G, Vasconcelos AT, Berlinck RGS, Thompson FL: Taxonomic and Functional Microbial Signatures of the Endemic Marine Sponge Arenosclera brasiliensis. ( 2012;7(7):e39905. doi: 10.1371/journal.pone.0039905).
4. Lucena BTL de, Silva GGZ, Santos BM dos, Dias GM, Amaral GRS, Moreira APB, Júnior MA de M, Dutilh BE, Edwards RA, Balbino V, Thompson CC, Thompson FL: Genome Sequences of the Ethanol-Tolerant Lactobacillus vini Strains LMG 23202T and JP7.8.9. ( 2012 Jun;194(11):3018. doi: 10.1128/JB.00446-12).